The purpose of this paper is to report the research and design of control system of magnetic coupling centrifugal blood pump in our laboratory, and to briefly describe the structure of the magnetic coupling centrifugal blood pump and principles of the body circulation model. The performance of blood pump is not only related to materials and structure, but also depends on the control algorithm. We studied the algorithm about motor current double-loop control for brushless DC motor. In order to make the algorithm adjust parameter change in different situations, we used the self-tuning fuzzy PI control algorithm and gave the details about how to design fuzzy rules. We mainly used Matlab Simulink to simulate the motor control system to test the performance of algorithm, and briefly introduced how to implement these algorithms in hardware system. Finally, by building the platform and conducting experiments, we proved that self-tuning fuzzy PI control algorithm could greatly improve both dynamic and static performance of blood pump and make the motor speed and the blood pump flow stable and adjustable.